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Tumor classification marker combination and application thereof

A biomarker and tumor technology, applied in lncRNA tumor classification marker combination and its application field, can solve problems such as unclear role of 5hmC

Active Publication Date: 2021-07-23
WENZHOU MEDICAL UNIV
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

However, the role of 5hmC on lncRNAs (long non-codingRNAs) is still unclear

Method used

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  • Tumor classification marker combination and application thereof
  • Tumor classification marker combination and application thereof
  • Tumor classification marker combination and application thereof

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0074] Example 1 5hmC epigenetic data set and data processing

[0075] 1. Sample source

[0076] Raw 5hmC data were collected for 261 samples, and the details of the samples are given in Table 1.

[0077] Table 1

[0078]

[0079] 2. Data processing

[0080] 5hmC sequencing reads were aligned to the human genome GRCh37 using Bowtie2 (version 2.3.4.2). Extremely abnormal samples were removed. Convert aligned sam files to bam files and sort using samtools. Unique non-duplicate matches to the genome are retained in picard. The release version (GRCh38 version) of the long non-coding RNA reference gene annotation file can be downloaded from the Gencode database. LiftOver was used to transfer localization information from the GRCh38 version to the GRCh37 version of the long non-coding RNA reference gene annotation file. Genes encoding lncRNAs were extracted based on GRCh37 annotations. From the fragment counts obtained in each RefSeq lncRNA, the read counts for 5hmC-modif...

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Abstract

The invention discloses a tumor classification marker combination and application thereof. Tumor classification plays a very important role in treatment of tumors, especially diagnosis and treatment of early tumors. At present, many researches focus on 5hmC distributed on a protein coding gene body and a promoter, but the effect of the 5hmC on the lncRNA is not clear yet, and through data analysis modeling, the tissue-specific 5hmC modified lncRNA is found, can be used as a tumor classification marker, and has important clinical application value.

Description

technical field [0001] The invention belongs to the field of biomedicine, and relates to a combination of tumor classification markers and applications thereof, and more specifically relates to a combination of tumor classification markers of lncRNA modified by 5hmC and its application. Background technique [0002] Different tumors correspond to potentially completely different treatment modalities. Tumor classification plays a very important role in the treatment of tumors. At present, the classification of early tumors still needs to be solved urgently. [0003] Many studies have shown that epigenetic abnormalities are closely related to the occurrence of tumors, senile diseases and developmental diseases. Therefore, epigenetic modification can be used as a new biomarker of disease, providing a new opportunity for the diagnosis and treatment of complex human diseases. cfDNA (circulating cell-free DNA) is a degraded DNA fragment released into plasma, which originates fro...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): C12Q1/6886C12M1/34C12M1/00
CPCC12Q1/6886C12Q2600/112C12Q2600/158C12Q2600/178
Inventor 苏建忠周猛侯萍孙杰
Owner WENZHOU MEDICAL UNIV